5 ms·

It's necessary to sequence all these so presumably they can be recreated if/when they go extinct.

schoen 8y ago
There's a drastically cheaper option for that: https://en.wikipedia.org/wiki/Gene_bank https://en.wikipedia.org/wiki/Gene_bank e.g. https://en.wikipedia.org/wiki/Seed_bank https://en.wikipedia.org/wiki/Seed_bank
- skookumchuck 8y ago
  But less reliable. Wasn't one of the seed banks in the arctic destroyed by flooding recently? Digital versions can be replicated and distributed at 0 cost.
  - xvedejas 8y ago
    Assuming you're referring to the Svalbard Global Seed Vault, the Wikipedia page answers your question: > In October 2016, the seed vault experienced an unusually large degree of water intrusion due to higher than average temperatures and heavy rainfall .... The vault was designed for water intrusion and as such the seeds were not at risk. The article's source: https://www.popsci.com/seed-vault-flooding https://www.popsci.com/seed-vault-flooding
    - skookumchuck 8y ago
      Thanks for the reference. We should indeed continue with seed vaults. But I'd feel better with a backup for that in the form of digital data.
      - maxander 8y ago
        If things go far enough downhill that the Svalbard vault is lost and its contents just allowed to rot, I’d be surprised if we retained the technological capacity to do things like synthesizing a complex genome from data. (I’m not sure we could do that with present technology either, for that matter.)
        skookumchuck 8y ago
        Libraries and museums burn down all the time, or get destroyed in wars. Consider the recent fire at the Hewlett-Packard museum, where all the paper history was lost. Nobody made a backup, even though paper lasts longer term than data on a hard drive. Frankly, I think storing data as ASCII in pits on a substrate is a great long term solution, as it can be read with a simple optical microscope, and ASCII is forever. One of the cool things about digital data is it can be copied forward limitlessly. Make the seed genomes public domain and put them on a server - people will make copies, like they make copies of wikipedia to store in their prepper bunkers.
        XorNot 8y ago
        I think UTF-8 is fine in this case since it's ASCII until it's not so you can write the UTF-8 spec out first. Human knowledge is more then English alphabet characters and not all concepts translate properly.
      - roywiggins 8y ago
        Even with the digital copy of the genome, you have to synthesize the entire genome, the cell it belongs in, and the rest of the seed to get a plant. That seems... possible, but hard enough that it doesn't make sense to call the sequenced genome a "backup".
        skookumchuck 8y ago
        It's infinitely better than having a photo of a wheat stalk.
panic 8y ago
Is it possible to recreate a wheat plant from just its genome?
- captain_perl 8y ago
  Today? No. Likely the so-called "junk DNA" was skipped over and we are still learning what the impact of environment and hormones is on gene expression. What we can do today is to manipulate DNA and re-inject into an egg. Although not nothing, this is not "just its genome." In 100 years? Probably.
- bohadi 8y ago
  A decent analogy might be: is it possible to recreate a running program from just it's source? (lacking a compiler, development and production environments, and perhaps user inputs) so my feeling is, not really, to an approximation
  - skookumchuck 8y ago
    Sure it's possible. (I've recreated programs from source despite lacking the compiler, etc., originally used on it. The trick is to adapt something else to the task.) The source contains instructions on how it works, and those instructions can be used elsewhere.
- eggie 8y ago
  No. You need a wheat cell as well. Then you might be in business. And, no, it is not possible (today) to rebuild a multi gigabase hexaploid genome. The best that's been done so far is mycoplasma (500kb genome, which is many orders of magnitude smaller). Also, the "genome sequence" presented here is not really complete. Thus far only the simplest organisms have had their genomes synthesized from a digital template and resulted in a viable cell. We rarely can produce a "complete" genome for anything other than bacteria and viruses. And for those, the diversity in the population makes the idea of establishing a single genome sequence somewhat limiting.
code_duck 8y ago
Seems like many other dire circumstances would have to befall the earth before any of the global top 3 crops become extinct.
- skookumchuck 8y ago
  There are many, many varieties of wheat. They all need to preserved, because they have many different strengths/weaknesses. Having a monoculture of crops is a terrible vulnerability. Look at what is happening with our current monoculture of bananas.
  - code_duck 8y ago
    As a longtime celiac sufferer, it would be in my best interest and that of my descendants for all of those varieties to be eradicated, like smallpox. There’s nothing especially beneficial about wheat as a food, and it has drawbacks, such as how it is the only food I can think of with its own autoimmune disease.
    - madengr 8y ago
      The article says wheat has 5x the human genome. I assume that means it’s very high in protein. Isn’t that what most of the world needs, as opposed to mostly carbohydrates?
      - code_duck 8y ago
        High in protein compared to what? Is wheat better than millet, sorghum, quinoa, teff, oats, corn, and rice, or is it just a European tradition to base cuisine on wheat? I’m not an agricultural or genetic expert and I have no idea what relation genome complexity has to proteins or how that makes it useful to humans. Overall wheat is not very high in protein... it’s a crop grown for carbohydrates. If you were trying to fulfill your daily protein needs from wheat, you’d fall quite short. I suppose it complements more adequate sources. The protein it does have - gluten - isn’t especially digestible compared to alternatives like corn or rice, though it does have a texture that people find pleasant or useful in baking. Crops like lentils and soy are what you grow if you want to grow protein.

There's a drastically cheaper option for that: https://en.wikipedia.org/wiki/Gene_bank https://en.wikipedia.org/wiki/Gene_bank e.g. https://en.wikipedia.org/wiki/Seed_bank https://en.wikipedia.org/wiki/Seed_bank

skookumchuck 8y ago
But less reliable. Wasn't one of the seed banks in the arctic destroyed by flooding recently? Digital versions can be replicated and distributed at 0 cost.
- xvedejas 8y ago
  Assuming you're referring to the Svalbard Global Seed Vault, the Wikipedia page answers your question: > In October 2016, the seed vault experienced an unusually large degree of water intrusion due to higher than average temperatures and heavy rainfall .... The vault was designed for water intrusion and as such the seeds were not at risk. The article's source: https://www.popsci.com/seed-vault-flooding https://www.popsci.com/seed-vault-flooding
  - skookumchuck 8y ago
    Thanks for the reference. We should indeed continue with seed vaults. But I'd feel better with a backup for that in the form of digital data.
    - maxander 8y ago
      If things go far enough downhill that the Svalbard vault is lost and its contents just allowed to rot, I’d be surprised if we retained the technological capacity to do things like synthesizing a complex genome from data. (I’m not sure we could do that with present technology either, for that matter.)
      - skookumchuck 8y ago
        Libraries and museums burn down all the time, or get destroyed in wars. Consider the recent fire at the Hewlett-Packard museum, where all the paper history was lost. Nobody made a backup, even though paper lasts longer term than data on a hard drive. Frankly, I think storing data as ASCII in pits on a substrate is a great long term solution, as it can be read with a simple optical microscope, and ASCII is forever. One of the cool things about digital data is it can be copied forward limitlessly. Make the seed genomes public domain and put them on a server - people will make copies, like they make copies of wikipedia to store in their prepper bunkers.
        XorNot 8y ago
        I think UTF-8 is fine in this case since it's ASCII until it's not so you can write the UTF-8 spec out first. Human knowledge is more then English alphabet characters and not all concepts translate properly.
    - roywiggins 8y ago
      Even with the digital copy of the genome, you have to synthesize the entire genome, the cell it belongs in, and the rest of the seed to get a plant. That seems... possible, but hard enough that it doesn't make sense to call the sequenced genome a "backup".
      - skookumchuck 8y ago
        It's infinitely better than having a photo of a wheat stalk.

panic 8y ago

Is it possible to recreate a wheat plant from just its genome?

captain_perl 8y ago
Today? No. Likely the so-called "junk DNA" was skipped over and we are still learning what the impact of environment and hormones is on gene expression. What we can do today is to manipulate DNA and re-inject into an egg. Although not nothing, this is not "just its genome." In 100 years? Probably.
bohadi 8y ago
A decent analogy might be: is it possible to recreate a running program from just it's source? (lacking a compiler, development and production environments, and perhaps user inputs) so my feeling is, not really, to an approximation
- skookumchuck 8y ago
  Sure it's possible. (I've recreated programs from source despite lacking the compiler, etc., originally used on it. The trick is to adapt something else to the task.) The source contains instructions on how it works, and those instructions can be used elsewhere.
eggie 8y ago
No. You need a wheat cell as well. Then you might be in business. And, no, it is not possible (today) to rebuild a multi gigabase hexaploid genome. The best that's been done so far is mycoplasma (500kb genome, which is many orders of magnitude smaller). Also, the "genome sequence" presented here is not really complete. Thus far only the simplest organisms have had their genomes synthesized from a digital template and resulted in a viable cell. We rarely can produce a "complete" genome for anything other than bacteria and viruses. And for those, the diversity in the population makes the idea of establishing a single genome sequence somewhat limiting.

code_duck 8y ago

Seems like many other dire circumstances would have to befall the earth before any of the global top 3 crops become extinct.

skookumchuck 8y ago
There are many, many varieties of wheat. They all need to preserved, because they have many different strengths/weaknesses. Having a monoculture of crops is a terrible vulnerability. Look at what is happening with our current monoculture of bananas.
- code_duck 8y ago
  As a longtime celiac sufferer, it would be in my best interest and that of my descendants for all of those varieties to be eradicated, like smallpox. There’s nothing especially beneficial about wheat as a food, and it has drawbacks, such as how it is the only food I can think of with its own autoimmune disease.
  - madengr 8y ago
    The article says wheat has 5x the human genome. I assume that means it’s very high in protein. Isn’t that what most of the world needs, as opposed to mostly carbohydrates?
    - code_duck 8y ago
      High in protein compared to what? Is wheat better than millet, sorghum, quinoa, teff, oats, corn, and rice, or is it just a European tradition to base cuisine on wheat? I’m not an agricultural or genetic expert and I have no idea what relation genome complexity has to proteins or how that makes it useful to humans. Overall wheat is not very high in protein... it’s a crop grown for carbohydrates. If you were trying to fulfill your daily protein needs from wheat, you’d fall quite short. I suppose it complements more adequate sources. The protein it does have - gluten - isn’t especially digestible compared to alternatives like corn or rice, though it does have a texture that people find pleasant or useful in baking. Crops like lentils and soy are what you grow if you want to grow protein.